背景:植物对冷胁迫的适应涉及与表观遗传调控相关的基因表达谱的变化。尽管三维(3D)基因组结构被认为是重要的表观遗传调节因子,3D基因组组织在冷应激反应中的作用尚不清楚.
结果:在这项研究中,我们使用Hi-C使用模型植物Brachypodiumdistachyon的对照和冷处理的叶片组织开发了高分辨率3D基因组图谱,以确定冷胁迫如何影响3D基因组结构。我们生成了〜1.5kb分辨率染色质相互作用图,并表明冷胁迫破坏不同水平的染色体组织,包括A/B舱过渡,染色质区隔化和拓扑关联域(TAD)大小的减少,和长程染色质环的丢失。整合RNA-seq信息,我们鉴定了冷反应基因,发现转录在很大程度上不受A/B区室转换的影响.冷反应基因主要位于A区室。TAD重组需要转录变化。我们证明动态TAD事件与H3K27me3和H3K27ac状态改变相关。此外,染色质循环的丢失,而不是循环的增益,与基因表达的改变相吻合,表明染色质环破坏在冷应激反应中可能比环形成起更重要的作用。
结论:我们的研究强调了冷胁迫期间发生的多尺度3D基因组重编程,并扩展了我们对植物响应冷胁迫的转录调控机制的认识。
BACKGROUND: The adaptation of plants to cold stress involves changes in gene expression profiles that are associated with epigenetic regulation. Although the three-dimensional (3D) genome architecture is considered an important epigenetic regulator, the role of 3D genome organization in the cold stress response remains unclear.
RESULTS: In this study, we developed high-resolution 3D genomic maps using control and cold-treated leaf tissue of the model plant Brachypodium distachyon using Hi-C to determine how cold stress affects the 3D genome architecture. We generated ~ 1.5 kb resolution chromatin interaction maps and showed that cold stress disrupts different levels of chromosome organization, including A/B compartment transition, a reduction in chromatin compartmentalization and the size of topologically associating domains (TADs), and loss of long-range chromatin loops. Integrating RNA-seq information, we identified cold-response genes and revealed that transcription was largely unaffected by the A/B compartment transition. The cold-response genes were predominantly localized in compartment A. In contrast, transcriptional changes are required for TAD reorganization. We demonstrated that dynamic TAD events were associated with H3K27me3 and H3K27ac state alterations. Moreover, a loss of chromatin looping, rather than a gain of looping, coincides with alterations in gene expression, indicating that chromatin loop disruption may play a more important role than loop formation in the cold-stress response.
CONCLUSIONS: Our study highlights the multiscale 3D genome reprogramming that occurs during cold stress and expands our knowledge of the mechanisms underlying transcriptional regulation in response to cold stress in plants.